In [1]:
import numpy as np
import pandas as pd
import math, re, os
import tensorflow as tf
DATA PRE-PROCESING STEP¶
Code for pre procssing taken from¶
https://www.kaggle.com/code/ryanholbrook/create-your-first-submission/notebook
In [2]:
print("TensorFlow version - "+tf.__version__)
# Detect TPU, return appropriate distribution strategy
try:
tpu = tf.distribute.cluster_resolver.TPUClusterResolver()
print('Running on TPU ', tpu.master())
except ValueError:
tpu = None
if tpu:
tf.config.experimental_connect_to_cluster(tpu)
tf.tpu.experimental.initialize_tpu_system(tpu)
strategy = tf.distribute.experimental.TPUStrategy(tpu)
else:
strategy = tf.distribute.get_strategy()
print("REPLICAS: ", strategy.num_replicas_in_sync)
Get DATA From KAGGLE¶
In [3]:
from kaggle_datasets import KaggleDatasets
GCS_DS_PATH = KaggleDatasets().get_gcs_path('tpu-getting-started')
print(GCS_DS_PATH) # what do gcs paths look like?
STEPS to convert data from tfrecords to readable format¶
In [4]:
IMAGE_SIZE = [512, 512]
GCS_PATH = GCS_DS_PATH + '/tfrecords-jpeg-512x512'
AUTO = tf.data.experimental.AUTOTUNE
TRAINING_FILENAMES = tf.io.gfile.glob(GCS_PATH + '/train/*.tfrec')
VALIDATION_FILENAMES = tf.io.gfile.glob(GCS_PATH + '/val/*.tfrec')
TEST_FILENAMES = tf.io.gfile.glob(GCS_PATH + '/test/*.tfrec')
CLASSES = ['pink primrose', 'hard-leaved pocket orchid', 'canterbury bells', 'sweet pea', 'wild geranium', 'tiger lily', 'moon orchid', 'bird of paradise', 'monkshood', 'globe thistle', # 00 - 09
'snapdragon', "colt's foot", 'king protea', 'spear thistle', 'yellow iris', 'globe-flower', 'purple coneflower', 'peruvian lily', 'balloon flower', 'giant white arum lily', # 10 - 19
'fire lily', 'pincushion flower', 'fritillary', 'red ginger', 'grape hyacinth', 'corn poppy', 'prince of wales feathers', 'stemless gentian', 'artichoke', 'sweet william', # 20 - 29
'carnation', 'garden phlox', 'love in the mist', 'cosmos', 'alpine sea holly', 'ruby-lipped cattleya', 'cape flower', 'great masterwort', 'siam tulip', 'lenten rose', # 30 - 39
'barberton daisy', 'daffodil', 'sword lily', 'poinsettia', 'bolero deep blue', 'wallflower', 'marigold', 'buttercup', 'daisy', 'common dandelion', # 40 - 49
'petunia', 'wild pansy', 'primula', 'sunflower', 'lilac hibiscus', 'bishop of llandaff', 'gaura', 'geranium', 'orange dahlia', 'pink-yellow dahlia', # 50 - 59
'cautleya spicata', 'japanese anemone', 'black-eyed susan', 'silverbush', 'californian poppy', 'osteospermum', 'spring crocus', 'iris', 'windflower', 'tree poppy', # 60 - 69
'gazania', 'azalea', 'water lily', 'rose', 'thorn apple', 'morning glory', 'passion flower', 'lotus', 'toad lily', 'anthurium', # 70 - 79
'frangipani', 'clematis', 'hibiscus', 'columbine', 'desert-rose', 'tree mallow', 'magnolia', 'cyclamen ', 'watercress', 'canna lily', # 80 - 89
'hippeastrum ', 'bee balm', 'pink quill', 'foxglove', 'bougainvillea', 'camellia', 'mallow', 'mexican petunia', 'bromelia', 'blanket flower', # 90 - 99
'trumpet creeper', 'blackberry lily', 'common tulip', 'wild rose'] # 100 - 102
def decode_image(image_data):
image = tf.image.decode_jpeg(image_data, channels=3)
image = tf.cast(image, tf.float32) / 255.0 # convert image to floats in [0, 1] range
image = tf.reshape(image, [*IMAGE_SIZE, 3]) # explicit size needed for TPU
return image
def read_labeled_tfrecord(example):
LABELED_TFREC_FORMAT = {
"image": tf.io.FixedLenFeature([], tf.string), # tf.string means bytestring
"class": tf.io.FixedLenFeature([], tf.int64), # shape [] means single element
}
example = tf.io.parse_single_example(example, LABELED_TFREC_FORMAT)
image = decode_image(example['image'])
label = tf.cast(example['class'], tf.int32)
return image, label # returns a dataset of (image, label) pairs
def read_unlabeled_tfrecord(example):
UNLABELED_TFREC_FORMAT = {
"image": tf.io.FixedLenFeature([], tf.string), # tf.string means bytestring
"id": tf.io.FixedLenFeature([], tf.string), # shape [] means single element
# class is missing, this competitions's challenge is to predict flower classes for the test dataset
}
example = tf.io.parse_single_example(example, UNLABELED_TFREC_FORMAT)
image = decode_image(example['image'])
idnum = example['id']
return image, idnum # returns a dataset of image(s)
def load_dataset(filenames, labeled=True, ordered=False):
# Read from TFRecords. For optimal performance, reading from multiple files at once and
# disregarding data order. Order does not matter since we will be shuffling the data anyway.
ignore_order = tf.data.Options()
if not ordered:
ignore_order.experimental_deterministic = False # disable order, increase speed
dataset = tf.data.TFRecordDataset(filenames, num_parallel_reads=AUTO) # automatically interleaves reads from multiple files
dataset = dataset.with_options(ignore_order) # uses data as soon as it streams in, rather than in its original order
dataset = dataset.map(read_labeled_tfrecord if labeled else read_unlabeled_tfrecord, num_parallel_calls=AUTO)
# returns a dataset of (image, label) pairs if labeled=True or (image, id) pairs if labeled=False
return dataset
In [5]:
def data_augment(image, label):
# Thanks to the dataset.prefetch(AUTO)
# statement in the next function (below), this happens essentially
# for free on TPU. Data pipeline code is executed on the "CPU"
# part of the TPU while the TPU itself is computing gradients.
image = tf.image.random_flip_left_right(image)
#image = tf.image.random_saturation(image, 0, 2)
return image, label
def get_training_dataset():
dataset = load_dataset(TRAINING_FILENAMES, labeled=True)
dataset = dataset.map(data_augment, num_parallel_calls=AUTO)
dataset = dataset.repeat() # the training dataset must repeat for several epochs
dataset = dataset.shuffle(2048)
dataset = dataset.batch(BATCH_SIZE)
dataset = dataset.prefetch(AUTO) # prefetch next batch while training (autotune prefetch buffer size)
return dataset
def get_validation_dataset(ordered=False):
dataset = load_dataset(VALIDATION_FILENAMES, labeled=True, ordered=ordered)
dataset = dataset.batch(BATCH_SIZE)
dataset = dataset.cache()
dataset = dataset.prefetch(AUTO)
return dataset
def get_test_dataset(ordered=False):
dataset = load_dataset(TEST_FILENAMES, labeled=False, ordered=ordered)
dataset = dataset.batch(BATCH_SIZE)
dataset = dataset.prefetch(AUTO)
return dataset
def count_data_items(filenames):
# the number of data items is written in the name of the .tfrec
# files, i.e. flowers00-230.tfrec = 230 data items
n = [int(re.compile(r"-([0-9]*)\.").search(filename).group(1)) for filename in filenames]
return np.sum(n)
NUM_TRAINING_IMAGES = count_data_items(TRAINING_FILENAMES)
NUM_VALIDATION_IMAGES = count_data_items(VALIDATION_FILENAMES)
NUM_TEST_IMAGES = count_data_items(TEST_FILENAMES)
print('Dataset: {} training images, {} validation images, {} unlabeled test images'.format(NUM_TRAINING_IMAGES, NUM_VALIDATION_IMAGES, NUM_TEST_IMAGES))
In [6]:
# Define the batch size. This will be 16 with TPU off and 128 (=16*8) with TPU on
BATCH_SIZE = 16 * strategy.num_replicas_in_sync
ds_train = get_training_dataset()
ds_valid = get_validation_dataset()
ds_test = get_test_dataset()
print("Training:", ds_train)
print ("Validation:", ds_valid)
print("Test:", ds_test)
In [7]:
np.set_printoptions(threshold=15, linewidth=80)
print("Training data shapes:")
for image, label in ds_train.take(3):
print(image.numpy().shape, label.numpy().shape)
print("Training data label examples:", label.numpy())
In [8]:
print("Test data shapes:")
for image, idnum in ds_test.take(3):
print(image.numpy().shape, idnum.numpy().shape)
print("Test data IDs:", idnum.numpy().astype('U')) # U=unicode string
Visualize the Data¶
In [9]:
from matplotlib import pyplot as plt
def batch_to_numpy_images_and_labels(data):
images, labels = data
numpy_images = images.numpy()
numpy_labels = labels.numpy()
if numpy_labels.dtype == object: # binary string in this case,
# these are image ID strings
numpy_labels = [None for _ in enumerate(numpy_images)]
# If no labels, only image IDs, return None for labels (this is
# the case for test data)
return numpy_images, numpy_labels
def title_from_label_and_target(label, correct_label):
if correct_label is None:
return CLASSES[label], True
correct = (label == correct_label)
return "{} [{}{}{}]".format(CLASSES[label], 'OK' if correct else 'NO', u"\u2192" if not correct else '',
CLASSES[correct_label] if not correct else ''), correct
def display_one_flower(image, title, subplot, red=False, titlesize=16):
plt.subplot(*subplot)
plt.axis('off')
plt.imshow(image)
if len(title) > 0:
plt.title(title, fontsize=int(titlesize) if not red else int(titlesize/1.2), color='red' if red else 'black', fontdict={'verticalalignment':'center'}, pad=int(titlesize/1.5))
return (subplot[0], subplot[1], subplot[2]+1)
def display_batch_of_images(databatch, predictions=None):
"""This will work with:
display_batch_of_images(images)
display_batch_of_images(images, predictions)
display_batch_of_images((images, labels))
display_batch_of_images((images, labels), predictions)
"""
# data
images, labels = batch_to_numpy_images_and_labels(databatch)
if labels is None:
labels = [None for _ in enumerate(images)]
# auto-squaring: this will drop data that does not fit into square
# or square-ish rectangle
rows = int(math.sqrt(len(images)))
cols = len(images)//rows
# size and spacing
FIGSIZE = 13.0
SPACING = 0.1
subplot=(rows,cols,1)
if rows < cols:
plt.figure(figsize=(FIGSIZE,FIGSIZE/cols*rows))
else:
plt.figure(figsize=(FIGSIZE/rows*cols,FIGSIZE))
# display
for i, (image, label) in enumerate(zip(images[:rows*cols], labels[:rows*cols])):
title = '' if label is None else CLASSES[label]
correct = True
if predictions is not None:
title, correct = title_from_label_and_target(predictions[i], label)
dynamic_titlesize = FIGSIZE*SPACING/max(rows,cols)*40+3 # magic formula tested to work from 1x1 to 10x10 images
subplot = display_one_flower(image, title, subplot, not correct, titlesize=dynamic_titlesize)
#layout
plt.tight_layout()
if label is None and predictions is None:
plt.subplots_adjust(wspace=0, hspace=0)
else:
plt.subplots_adjust(wspace=SPACING, hspace=SPACING)
plt.show()
def display_training_curves(training, validation, title, subplot):
if subplot%10==1: # set up the subplots on the first call
plt.subplots(figsize=(10,10), facecolor='#F0F0F0')
plt.tight_layout()
ax = plt.subplot(subplot)
ax.set_facecolor('#F8F8F8')
ax.plot(training)
ax.plot(validation)
ax.set_title('model '+ title)
ax.set_ylabel(title)
#ax.set_ylim(0.28,1.05)
ax.set_xlabel('epoch')
ax.legend(['train', 'valid.'])
In [10]:
ds_iter = iter(ds_train.unbatch().batch(20))
In [11]:
one_batch = next(ds_iter)
display_batch_of_images(one_batch)
CREATE THE MODEL¶
Contribution¶
Model generated with batch normalization followed by 4 2d convolutions and maxpooling after each 2d convolution
In [12]:
EPOCHS = 8
model = tf.keras.Sequential([
# tf.keras.layers.Rescaling(1./255,input_shape =(*IMAGE_SIZE,3)),
tf.keras.layers.BatchNormalization(input_shape = (*IMAGE_SIZE,3)),
tf.keras.layers.Conv2D(16,3,padding='same',activation='relu'),
tf.keras.layers.MaxPool2D(),
tf.keras.layers.Conv2D(32,3,padding='same',activation='relu'),
tf.keras.layers.MaxPool2D(),
tf.keras.layers.Conv2D(64,3,padding='same',activation='relu'),
tf.keras.layers.MaxPool2D(),
tf.keras.layers.Conv2D(128,3,padding='same',activation='relu'),
tf.keras.layers.MaxPool2D(),
tf.keras.layers.Flatten(),
tf.keras.layers.Dense(len(CLASSES), activation='softmax')
])
In [13]:
model.compile(
optimizer='adam',
loss = 'sparse_categorical_crossentropy',
metrics=['sparse_categorical_accuracy'],
)
model.summary()
Set learning rate and visualize the graph¶
In [14]:
# Learning Rate Schedule for Fine Tuning #
def exponential_lr(epoch,
start_lr = 0.0000001, min_lr = 0.0000001, max_lr = 0.0000005,
rampup_epochs = 5, sustain_epochs = 0,
exp_decay = 0.8):
def lr(epoch, start_lr, min_lr, max_lr, rampup_epochs, sustain_epochs, exp_decay):
# linear increase from start to rampup_epochs
if epoch < rampup_epochs:
lr = ((max_lr - start_lr) /
rampup_epochs * epoch + start_lr)
# constant max_lr during sustain_epochs
elif epoch < rampup_epochs + sustain_epochs:
lr = max_lr
# exponential decay towards min_lr
else:
lr = ((max_lr - min_lr) *
exp_decay**(epoch - rampup_epochs - sustain_epochs) +
min_lr)
return lr
return lr(epoch,
start_lr,
min_lr,
max_lr,
rampup_epochs,
sustain_epochs,
exp_decay)
lr_callback = tf.keras.callbacks.LearningRateScheduler(exponential_lr, verbose=True)
rng = [i for i in range(EPOCHS)]
y = [exponential_lr(x) for x in rng]
plt.plot(rng, y)
print("Learning rate schedule: {:.3g} to {:.3g} to {:.3g}".format(y[0], max(y), y[-1]))
In [15]:
# Define training epochs
EPOCHS = 8
STEPS_PER_EPOCH = NUM_TRAINING_IMAGES // BATCH_SIZE
history = model.fit(
ds_train,
validation_data=ds_valid,
epochs=EPOCHS,
steps_per_epoch=STEPS_PER_EPOCH,
callbacks=[lr_callback],
)
In [16]:
display_training_curves(
history.history['loss'],
history.history['val_loss'],
'loss',
211,
)
display_training_curves(
history.history['sparse_categorical_accuracy'],
history.history['val_sparse_categorical_accuracy'],
'accuracy',
212,
)
In [17]:
import matplotlib.pyplot as plt
from sklearn.metrics import f1_score, precision_score, recall_score, confusion_matrix
def display_confusion_matrix(cmat, score, precision, recall):
plt.figure(figsize=(15,15))
ax = plt.gca()
ax.matshow(cmat, cmap='Reds')
ax.set_xticks(range(len(CLASSES)))
ax.set_xticklabels(CLASSES, fontdict={'fontsize': 7})
plt.setp(ax.get_xticklabels(), rotation=45, ha="left", rotation_mode="anchor")
ax.set_yticks(range(len(CLASSES)))
ax.set_yticklabels(CLASSES, fontdict={'fontsize': 7})
plt.setp(ax.get_yticklabels(), rotation=45, ha="right", rotation_mode="anchor")
titlestring = ""
if score is not None:
titlestring += 'f1 = {:.3f} '.format(score)
if precision is not None:
titlestring += '\nprecision = {:.3f} '.format(precision)
if recall is not None:
titlestring += '\nrecall = {:.3f} '.format(recall)
if len(titlestring) > 0:
ax.text(101, 1, titlestring, fontdict={'fontsize': 18, 'horizontalalignment':'right', 'verticalalignment':'top', 'color':'#804040'})
plt.show()
def display_training_curves(training, validation, title, subplot):
if subplot%10==1: # set up the subplots on the first call
plt.subplots(figsize=(10,10), facecolor='#F0F0F0')
plt.tight_layout()
ax = plt.subplot(subplot)
ax.set_facecolor('#F8F8F8')
ax.plot(training)
ax.plot(validation)
ax.set_title('model '+ title)
ax.set_ylabel(title)
#ax.set_ylim(0.28,1.05)
ax.set_xlabel('epoch')
ax.legend(['train', 'valid.'])
In [18]:
cmdataset = get_validation_dataset(ordered=True)
images_ds = cmdataset.map(lambda image, label: image)
labels_ds = cmdataset.map(lambda image, label: label).unbatch()
cm_correct_labels = next(iter(labels_ds.batch(NUM_VALIDATION_IMAGES))).numpy()
cm_probabilities = model.predict(images_ds)
cm_predictions = np.argmax(cm_probabilities, axis=-1)
labels = range(len(CLASSES))
cmat = confusion_matrix(
cm_correct_labels,
cm_predictions,
labels=labels,
)
cmat = (cmat.T / cmat.sum(axis=1)).T # normalize
In [19]:
score = f1_score(
cm_correct_labels,
cm_predictions,
labels=labels,
average='macro',
)
precision = precision_score(
cm_correct_labels,
cm_predictions,
labels=labels,
average='macro',
)
recall = recall_score(
cm_correct_labels,
cm_predictions,
labels=labels,
average='macro',
)
display_confusion_matrix(cmat, score, precision, recall)
In [20]:
dataset = get_validation_dataset()
dataset = dataset.unbatch().batch(20)
batch = iter(dataset)
In [21]:
images, labels = next(batch)
probabilities = model.predict(images)
predictions = np.argmax(probabilities, axis=-1)
display_batch_of_images((images, labels), predictions)
In [22]:
test_ds = get_test_dataset(ordered=True)
print('Computing predictions...')
test_images_ds = test_ds.map(lambda image, idnum: image)
probabilities = model.predict(test_images_ds)
predictions = np.argmax(probabilities, axis=-1)
print(predictions)
In [23]:
print('Generating submission.csv file...')
# Get image ids from test set and convert to unicode
test_ids_ds = test_ds.map(lambda image, idnum: idnum).unbatch()
test_ids = next(iter(test_ids_ds.batch(NUM_TEST_IMAGES))).numpy().astype('U')
# Write the submission file
np.savetxt(
'submission.csv',
np.rec.fromarrays([test_ids, predictions]),
fmt=['%s', '%d'],
delimiter=',',
header='id,label',
comments='',
)
# Look at the first few predictions
!head submission.csv
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